derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.

AuthorLeonardo Collado-Torres [aut, cre], Alyssa C. Frazee [ctb], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]
Date of publicationNone
MaintainerLeonardo Collado-Torres <lcollado@jhu.edu>
LicenseArtistic-2.0
Version1.8.0
https://github.com/lcolladotor/derfinder

View on Bioconductor

Man pages

analyzeChr: Run the derfinder analysis on a chromosome

annotateRegions: Assign genomic states to regions

calculatePvalues: Calculate p-values and identify regions

calculateStats: Calculate F-statistics at base pair resolution from a loaded...

coerceGR: Coerce the coverage to a GRanges object for a given sample

collapseFullCoverage: Collapse full coverage information for efficient quantile...

coverageToExon: Extract coverage information for exons

createBw: Export coverage to BigWig files

createBwSample: Create a BigWig file with the coverage information for a...

define_cluster: Define a cluster to use.

derfinder-deprecated: Deprecated functions in package 'derfinder'

derfinder-package: Annotation-agnostic differential expression analysis of...

extendedMapSeqlevels: Change naming style for a set of sequence names

filterData: Filter the positions of interest

findRegions: Find non-zero regions in a Rle

fullCoverage: Load the unfiltered coverage information from a group of BAM...

genomeData: Genome samples processed data

genomeDataRaw: Genome samples processed data

genomeFstats: F-statistics for the example data

genomeInfo: Genome samples information

genomeRegions: Candidate DERs for example data

genomicState: Genomic State for Hsapiens.UCSC.hg19.knownGene

getRegionCoverage: Extract coverage information for a set of regions

getTotalMapped: Calculate the total number of mapped reads

loadCoverage: Load the coverage information from a group of BAM files

makeGenomicState: Obtain the genomic state per region from annotation

makeModels: Build model matrices for differential expression

mergeResults: Merge results from different chromosomes

preprocessCoverage: Transform and split the data

railMatrix: Identify regions data by a coverage filter and get a count...

rawFiles: Construct full paths to a group of raw input files

regionMatrix: Identify regions data by a coverage filter and get a count...

sampleDepth: Calculate adjustments for library size

Functions

advancedArg Man page
analyzeChr Man page
annotateRegions Man page
calculatePvalues Man page
calculateStats Man page
coerceGR Man page
collapseFullCoverage Man page
coverageToExon Man page
createBw Man page
createBwSample Man page
define_cluster Man page
derfinder-deprecated Man page
derfinder-package Man page
extendedMapSeqlevels Man page
filterData Man page
findRegions Man page
fullCoverage Man page
genomeData Man page
genomeDataRaw Man page
genomeFstats Man page
genomeInfo Man page
genomeRegions Man page
genomicState Man page
getRegionCoverage Man page
getTotalMapped Man page
loadCoverage Man page
makeGenomicState Man page
makeModels Man page
mergeResults Man page
preprocessCoverage Man page
railMatrix Man page
rawFiles Man page
regionMatrix Man page
sampleDepth Man page

Files

derfinder/DESCRIPTION
derfinder/NAMESPACE
derfinder/NEWS
derfinder/R
derfinder/R/Deprecated.R derfinder/R/analyzeChr.R derfinder/R/annotateRegions.R derfinder/R/calculatePvalues.R derfinder/R/calculateStats.R derfinder/R/coerceGR.R derfinder/R/collapseFullCoverage.R derfinder/R/coverageToExon.R derfinder/R/createBw.R derfinder/R/createBwSample.R derfinder/R/define_cluster.R derfinder/R/derfinder-package.R derfinder/R/extendedMapSeqlevels.R derfinder/R/filterData.R derfinder/R/findRegions.R derfinder/R/fullCoverage.R derfinder/R/genomeData-data.R derfinder/R/genomeDataRaw-data.R derfinder/R/genomeFstats-data.R derfinder/R/genomeInfo-data.R derfinder/R/genomeRegions-data.R derfinder/R/genomicState-data.R derfinder/R/getRegionCoverage.R derfinder/R/getTotalMapped.R derfinder/R/loadCoverage.R derfinder/R/makeGenomicState.R derfinder/R/makeModels.R derfinder/R/mergeResults.R derfinder/R/preprocessCoverage.R derfinder/R/railMatrix.R derfinder/R/rawFiles.R derfinder/R/regionMatrix.R derfinder/R/sampleDepth.R derfinder/R/utils.R
derfinder/README.md
derfinder/build
derfinder/build/vignette.rds
derfinder/data
derfinder/data/genomeData.RData
derfinder/data/genomeDataRaw.RData
derfinder/data/genomeFstats.RData
derfinder/data/genomeInfo.RData
derfinder/data/genomeRegions.RData
derfinder/data/genomicState.RData
derfinder/inst
derfinder/inst/CITATION
derfinder/inst/doc
derfinder/inst/doc/derfinder-quickstart.R
derfinder/inst/doc/derfinder-quickstart.Rmd
derfinder/inst/doc/derfinder-quickstart.html
derfinder/inst/doc/derfinder-users-guide.R
derfinder/inst/doc/derfinder-users-guide.Rmd
derfinder/inst/doc/derfinder-users-guide.html
derfinder/inst/extdata
derfinder/inst/extdata/chr21
derfinder/inst/extdata/chr21/annotation.Rdata
derfinder/inst/extdata/chr21/coveragePrep.Rdata
derfinder/inst/extdata/chr21/fstats.Rdata
derfinder/inst/extdata/chr21/optionsStats.Rdata
derfinder/inst/extdata/chr21/regions.Rdata
derfinder/inst/extdata/chr21/timeinfo.Rdata
derfinder/inst/extdata/genomeData
derfinder/inst/extdata/genomeData/ERR009101_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009101_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009102_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009102_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009105_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009105_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009107_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009107_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009108_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009108_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009112_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009112_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009115_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009115_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009116_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009116_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009131_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009131_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009138_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009138_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009144_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009144_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009145_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009145_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009148_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009148_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009151_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009151_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009152_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009152_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009153_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009153_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009159_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009159_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009161_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009161_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009163_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009163_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009164_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009164_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/ERR009167_accepted_hits.bam
derfinder/inst/extdata/genomeData/ERR009167_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031812_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031812_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031835_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031835_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031867_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031867_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031868_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031868_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031900_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031900_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031904_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031904_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031914_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031914_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031936_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031936_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031958_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031958_accepted_hits.bam.bai
derfinder/inst/extdata/genomeData/SRR031960_accepted_hits.bam
derfinder/inst/extdata/genomeData/SRR031960_accepted_hits.bam.bai
derfinder/man
derfinder/man/analyzeChr.Rd derfinder/man/annotateRegions.Rd derfinder/man/calculatePvalues.Rd derfinder/man/calculateStats.Rd derfinder/man/coerceGR.Rd derfinder/man/collapseFullCoverage.Rd derfinder/man/coverageToExon.Rd derfinder/man/createBw.Rd derfinder/man/createBwSample.Rd derfinder/man/define_cluster.Rd derfinder/man/derfinder-deprecated.Rd derfinder/man/derfinder-package.Rd derfinder/man/extendedMapSeqlevels.Rd derfinder/man/filterData.Rd derfinder/man/findRegions.Rd derfinder/man/fullCoverage.Rd derfinder/man/genomeData.Rd derfinder/man/genomeDataRaw.Rd derfinder/man/genomeFstats.Rd derfinder/man/genomeInfo.Rd derfinder/man/genomeRegions.Rd derfinder/man/genomicState.Rd derfinder/man/getRegionCoverage.Rd derfinder/man/getTotalMapped.Rd derfinder/man/loadCoverage.Rd derfinder/man/makeGenomicState.Rd derfinder/man/makeModels.Rd derfinder/man/mergeResults.Rd derfinder/man/preprocessCoverage.Rd derfinder/man/railMatrix.Rd derfinder/man/rawFiles.Rd derfinder/man/regionMatrix.Rd derfinder/man/sampleDepth.Rd
derfinder/tests
derfinder/tests/test-all.R
derfinder/tests/testthat
derfinder/tests/testthat/test_ER_level.R
derfinder/tests/testthat/test_Fstats.R
derfinder/tests/testthat/test_annotation.R
derfinder/tests/testthat/test_data.R
derfinder/tests/testthat/test_findRegions.R
derfinder/tests/testthat/test_misc.R
derfinder/vignettes
derfinder/vignettes/derfinder-quickstart.Rmd
derfinder/vignettes/derfinder-users-guide.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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